Rowan MCP Server

MCP server for making it easy to run Rowan's molecular design and simulation tools.

Installation

Option 1: Auto-Install (No manual installation needed!)

Just add this to your MCP configuration and it will automatically install and run:

HTTP/SSE configuration:

{
  "mcpServers": {
    "rowan": {
      "type": "http",
      "url": "http://127.0.0.1:6276/sse"
    }
  }
}

Then start the server:

# Set your API key
export ROWAN_API_KEY="your_api_key_here"

# Start the HTTP server
uvx --from rowan-mcp rowan-mcp

Option 2: Manual Installation

If you prefer to install the package first:

Using uv:

uv add rowan-mcp

Using pip:

pip install rowan-mcp

Then configure and start:

{
  "mcpServers": {
    "rowan": {
      "type": "http", 
      "url": "http://127.0.0.1:6276/sse"
    }
  }
}

# Set API key and start server
export ROWAN_API_KEY="your_api_key_here"
rowan-mcp

Get API Key

Visit labs.rowansci.com → Create account → Generate API key

Start Using

Ask your AI: "Calculate the pKa of aspirin" or "Optimize the geometry of caffeine"

What You Can Do

Ask the LLM to:

Calculate drug properties: "Predict drug-likeness of aspirin"
Optimize molecular structures: "Optimize the geometry of aspirin"
Predict chemical behavior: "What's the pKa of acetic acid?"
Run calculations: "Calculate the HOMO and LUMO of benzene"

System Requirements

Python 3.11+
Package manager: uv (recommended) or pip
Rowan API key (free at labs.rowansci.com)
MCP-compatible client (Claude Desktop, etc.)

Development commands (if you cloned the repo):

# Run from source
export ROWAN_API_KEY="your_api_key_here"
uv run python -m rowan_mcp

Available Tools

Total: 45 MCP Tools

28 Dedicated Workflow Functions (all workflows from Rowan v2.1.9)
1 Batch Workflow Function
3 Molecule Lookup Tools
7 Workflow Management Tools
6 Protein Management Tools

Chemistry Calculations

submit_basic_calculation_workflow - Energy, optimization, frequencies with multiple engines (omol25, xtb, psi4)
submit_conformer_search_workflow - Conformational search with multiple search modes (rapid/careful/meticulous)
submit_conformers_workflow - Conformer generation and enumeration (different from conformer_search)
submit_multistage_opt_workflow - Multi-stage geometry optimization with sequential accuracy levels
submit_scan_workflow - Molecular scans (dihedral, bond, angle) with wavefront propagation
submit_irc_workflow - Intrinsic reaction coordinate calculations for transition states

Molecular Properties

submit_pka_workflow - Microscopic pKa calculations with customizable pH ranges and elements
submit_macropka_workflow - Macroscopic pKa calculations across pH and charge ranges
submit_solubility_workflow - Solubility predictions across multiple solvents and temperatures
submit_redox_potential_workflow - Electrochemical reduction/oxidation potentials
submit_descriptors_workflow - ML-ready molecular descriptors and features
submit_tautomer_search_workflow - Tautomer enumeration
submit_admet_workflow - ADME/Tox property predictions for drug discovery
submit_hydrogen_bond_basicity_workflow - Hydrogen bond basicity (pKBHX) predictions

Reactivity Analysis

submit_fukui_workflow - Fukui indices for electrophilic/nucleophilic reactivity sites

Electronic Structure

submit_spin_states_workflow - Spin state energy calculations for different multiplicities

Spectroscopy & Analysis

submit_ion_mobility_workflow - Ion mobility mass spectrometry collision cross-section (CCS) predictions
submit_strain_workflow - Molecular strain energy calculations for rings and cages

Transition States & Reactions

submit_double_ended_ts_search_workflow - Transition state search from reactant and product structures
submit_pose_analysis_md_workflow - Molecular dynamics simulations on docked protein-ligand complexes

Protein & Drug Discovery

submit_docking_workflow - Protein-ligand docking with multiple executables (Vina, QVina2, Smina)
submit_batch_docking_workflow - High-throughput docking for virtual screening campaigns
submit_protein_cofolding_workflow - Multi-protein and protein-ligand cofolding predictions
submit_msa_workflow - Multiple sequence alignment for protein structure prediction

Batch Processing

batch_submit_workflow - Submit multiple molecules through any workflow type for high-throughput processing

Molecule Management

molecule_lookup - Convert molecule names, CAS numbers, IUPAC names to SMILES
batch_molecule_lookup - Bulk molecule name to SMILES conversion
validate_smiles - Validate and standardize SMILES strings

Protein Management

create_protein_from_pdb_id - Create protein from PDB ID (e.g., '1HCK')
retrieve_protein - Get protein data by UUID
list_proteins - List all available proteins
upload_protein - Upload custom protein structures
delete_protein - Remove protein from workspace
sanitize_protein - Clean and validate protein structures

Workflow Management

retrieve_workflow - Get complete workflow data, status, and results (single source of truth)
workflow_stop - Stop running workflows
workflow_delete - Remove workflows from workspace
retrieve_calculation_molecules - Extract molecular structures from calculations
list_workflows - List all workflows with filtering options
workflow_update - Modify workflow parameters
workflow_delete_data - Remove workflow data while keeping metadata

Requirements

Python 3.11+
Rowan API key
MCP-compatible AI assistant (Claude Desktop, etc.)

Experimental: Desktop Extension (Work in Progress)

Working on a one-click desktop extension (.dxt) for Claude Desktop that eliminates command-line setup! This feature is currently being refined for compatibility with the MCP extension system.

For now, use the standard Package Installation method above, which is fully tested and reliable.

Getting Help

Documentation: docs.rowansci.com
or ping me!

Citation

If you use this MCP tool in your research, please cite the underlying Rowan platform:

Rowan Scientific. https://www.rowansci.com (accessed 2025-07-01).

For complete citation information including specific computational engines, methods, and workflows used in your calculations, please refer to Rowan's citation guidelines.

Publishing (Maintainer Notes)

To publish a new version to PyPI:

# Update version in pyproject.toml and rowan_mcp/__init__.py
# Build the package
uv build

# Publish to PyPI (requires API token)
uv publish

# Or publish to TestPyPI first
uv publish --index-url https://test.pypi.org/simple/

MCP inspector

# Start the server first
export ROWAN_API_KEY="your_api_key_here" 
uv run python -m rowan_mcp &

# Then inspect
npx @modelcontextprotocol/inspector http://127.0.0.1:6276/sse